SMTL ID : 8hfz.1

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with white-tailed deer ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

21 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: T.108, N.234, I.235, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.709 Chain B: I.794, D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: Y.707, N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.801, S.803, Q.804, G.932 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: S.708, S.711, N.1074, T.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain A: I.794, D.796 Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: N.801, F.802, S.803, Q.804, N.928 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.706 NAG-NAG.19: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain D: K.400, A.401, N.527 No protein-ligand interaction detected (PLIP)

23 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.22: 3 residues within 4Å: Chain A: Y.28, N.61, H.625 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.122, A.123, N.125 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: G.339, N.343 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.616, T.618, E.619 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: C.15, N.17, C.136, N.137 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: R.357, Y.396 Chain B: E.132, N.165 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain C: N.17, R.21, D.138, F.140, R.246, W.258 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, F.157 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Q.115, N.165 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: G.339, F.342, N.343, N.370, S.371 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.42: 7 residues within 4Å: Chain D: W.30, N.31, T.34, N.35, N.40, R.321, K.322 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: E.411, N.413 Ligand excluded by PLIP NAG.44: 7 residues within 4Å: Chain D: E.4, K.8, I.70, Q.71, N.72, T.74, L.75 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.45: 3 residues within 4Å: Chain D: H.355, H.359, E.383 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.355, D:H.359, D:H.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, P. et al., Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. J.Virol. (2023)

Release Date

2023-08-30

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

Spike glycoprotein

Angiotensin-converting enzyme

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